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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ), 'gf_id' => 'HOM05D001405', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001405' ), 'data_identifier' => 'HOM05D001405', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001405', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '446', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p21390' => 'bna', 'A06p05730' => 'bna', 'A07p18720' => 'bna', 'A09p65750' => 'bna', 'A10p21400' => 'bna', 'Aa31LG11G11500' => 'aar', 'Aa31LG5G7940' => 'aar', 'Aa31sc17G240' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.818' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1298' => 'aag', 'Actinidia00056' => 'ach', 'Actinidia07185' => 'ach', 'Actinidia23437' => 'ach', 'Actinidia24147' => 'ach', 'Actinidia32383' => 'ach', 'Actinidia38609' => 'ach', 'Ah.01g014110' => 'amhyb', 'Ah.04g153120' => 'amhyb', 'Ah.04g160010' => 'amhyb', 'AL1G19260' => 'aly', 'AL4G21940' => 'aly', 'AL6G29300' => 'aly', 'Aqoxy2G00518' => 'aox', 'Aqoxy2G01655' => 'aox', 'Aqoxy2G03130' => 'aox', 'Aqoxy4G01649' => 'aox', 'Aqoxy5G00627' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0B901Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0T503U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43HVBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.43MM9Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7MJR1K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7W72E0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8W91IE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AE8RBB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CHB81T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2HDNA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5G7QD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QEYP2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R44NGB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U5CAXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4C5VP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XU9CUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YY2QIM' => 'arhy', 'AT1G08830' => 'ath', 'AT2G28190' => 'ath', 'AT5G18100' => 'ath', 'ATR0329G010' => 'atr', 'ATR0706G086' => 'atr', 'ATR0737G039' => 'atr', 'Atru.chr2.627' => 'acertr', 'Atru.chr3.3507' => 'acertr', 'Atru.chr3.3514' => 'acertr', 'Atru.chr9.2566' => 'acertr', 'AUR62000929' => 'cqu', 'AUR62005041' => 'cqu', 'AUR62014976' => 'cqu', 'AUR62029152' => 'cqu', 'AUR62032030' => 'cqu', 'AUR62032721' => 'cqu', 'BcaB02g10154' => 'bca', 'BcaB06g28194' => 'bca', 'BcaB08g36706' => 'bca', 'BcaC01g05094' => 'bca', 'BcaC02g08201' => 'bca', 'BcaC04g18724' => 'bca', 'BcaC05g24743' => 'bca', 'BcaC07g41924' => 'bca', 'BolC4t27259H' => 'bol', 'BolC5t29449H' => 'bol', 'BolC8t52509H' => 'bol', 'BolC9t57575H' => 'bol', 'BolC9t58732H' => 'bol', 'BraA04t17706Z' => 'bra', 'BraA06t23783Z' => 'bra', 'BraA07t29582Z' => 'bra', 'BraA09t41918Z' => 'bra', 'BraA10t44203Z' => 'bra', 'C04p57340' => 'bna', 'C05p06920' => 'bna', 'C08p49820' => 'bna', 'C09p58880' => 'bna', 'CAN.G223.4' => 'can', 'CAN.G503.1' => 'can', 'CAN.G546.49' => 'can', 'CAN.G904.37' => 'can', 'CANSAT54G0059' => 'cansat', 'CANSAT64G0315' => 'cansat', 'CANSAT78G0810' => 'cansat', 'CARHR008750' => 'chi', 'CARHR121080' => 'chi', 'CARHR194970' => 'chi', 'Carub.0001s0818' => 'cru', 'Carub.0004s0900' => 'cru', 'Carub.0006s1639' => 'cru', 'Ca_04481_v3' => 'car', 'Ca_09390_v3' => 'car', 'Ca_19321_v3' => 'car', 'CBR_g3018' => 'cbr', 'Cc01_g10280' => 'ccan', 'Cc02_g32280' => 'ccan', 'Cc03_g02460' => 'ccan', 'Cc06_g23140' => 'ccan', 'Cc06_g23170' => 'ccan', 'CDE01G0498' => 'cde', 'CDE12G0305' => 'cde', 'Cfa017657' => 'cfa', 'Ciclev10002619m.g' => 'ccl', 'Ciclev10002663m.g' => 'ccl', 'Ciclev10002756m.g' => 'ccl', 'Ciclev10002905m.g' => 'ccl', 'Ciclev10022494m.g' => 'ccl', 'Ciclev10029196m.g' => 'ccl', 'Ciclev10029488m.g' => 'ccl', 'CiPaw.04G171700' => 'cil', 'CiPaw.07G011000' => 'cil', 'CiPaw.08G105900' => 'cil', 'CiPaw.10G127200' => 'cil', 'CiPaw.12G001300' => 'cil', 'CiPaw.13G122800' => 'cil', 'CiPaw.14G088600' => 'cil', 'CiPaw.15G152000' => 'cil', 'CiPaw.16G024800' => 'cil', 'ClCG02G016260' => 'cla', 'ClCG02G021620' => 'cla', 'ClCG03G016470' => 'cla', 'ClCG04G005370' => 'cla', 'COL.COLO4_07330' => 'col', 'COL.COLO4_19195' => 'col', 'COL.COLO4_36053' => 'col', 'Cpa.g.sc1.4' => 'cpa', 'Cpa.g.sc117.11' => 'cpa', 'Cpa.g.sc51.134' => 'cpa', 'CsaV3_1G039510' => 'csa', 'CsaV3_2G004490' => 'csa', 'CsaV3_4G013220' => 'csa', 'CsaV3_6G014400' => 'csa', 'CSS0007322' => 'camsi', 'CSS0007453' => 'camsi', 'CSS0009283' => 'camsi', 'CSS0017734' => 'camsi', 'CSS0026139' => 'camsi', 'CSS0026503' => 'camsi', 'CSS0036639' => 'camsi', 'CSS0045115' => 'camsi', 'DCAR_002436' => 'dca', 'DCAR_003297' => 'dca', 'DCAR_015506' => 'dca', 'DCAR_017048' => 'dca', 'DCAR_030571' => 'dca', 'Dinv03427' => 'din', 'Dinv16224' => 'din', 'Dinv27606' => 'din', 'Dinv29381' => 'din', 'Dinv37023' => 'din', 'Dinv44436' => 'din', 'Duzib106G0775' => 'dzi', 'Duzib128G1007' => 'dzi', 'Duzib150G0374' => 'dzi', 'Duzib170G0604' => 'dzi', 'Duzib177G0098' => 'dzi', 'Duzib177G0486' => 'dzi', 'ECA233G0579' => 'eca', 'ECA233G4942' => 'eca', 'ECA238G0961' => 'eca', 'ECA238G1616' => 'eca', 'EL10Ac3g06832' => 'bvu', 'EL10Ac4g09246' => 'bvu', 'EL10Ac9g22624' => 'bvu', 'Eucgr.A02107' => 'egr', 'Eucgr.B01760' => 'egr', 'Eucgr.B03930' => 'egr', 'Eucgr.H04426' => 'egr', 'FAN02G1379' => 'fan', 'FAN09G1221' => 'fan', 'FAN11G2631' => 'fan', 'FAN14G3909' => 'fan', 'FAN16G0003' => 'fan', 'FAN21G4010' => 'fan', 'FAN23G2730' => 'fan', 'FAN25G0913' => 'fan', 'FAN26G1435' => 'fan', 'FvH4_1g28280' => 'fve', 'FvH4_3g30620' => 'fve', 'FvH4_6g04231' => 'fve', 'Glyma.03G242900' => 'gma', 'Glyma.11G192700' => 'gma', 'Glyma.12G081300' => 'gma', 'Glyma.12G178800' => 'gma', 'Glyma.16G153900' => 'gma', 'Glyma.19G240400' => 'gma', 'Gohir.A05G086900' => 'ghi', 'Gohir.A09G088700' => 'ghi', 'Gohir.A11G234400' => 'ghi', 'Gohir.A13G100600' => 'ghi', 'Gohir.A13G166100' => 'ghi', 'Gohir.D05G088150' => 'ghi', 'Gohir.D09G088400' => 'ghi', 'Gohir.D11G245400' => 'ghi', 'Gohir.D13G104200' => 'ghi', 'Gohir.D13G169000' => 'ghi', 'Gorai.006G104900' => 'gra', 'Gorai.007G261100' => 'gra', 'Gorai.009G090300' => 'gra', 'Gorai.013G116800' => 'gra', 'Gorai.013G192900' => 'gra', 'GSVIVG01008611001' => 'vvi', 'GSVIVG01021922001' => 'vvi', 'GSVIVG01021932001' => 'vvi', 'GSVIVG01021949001' => 'vvi', 'GSVIVG01021953001' => 'vvi', 'GSVIVG01021959001' => 'vvi', 'GSVIVG01023414001' => 'vvi', 'GSVIVG01031462001' => 'vvi', 'GSVIVG01033413001' => 'vvi', 'HanXRQChr02g0055581' => 'han', 'HanXRQChr07g0190131' => 'han', 'HanXRQChr08g0227691' => 'han', 'HanXRQChr14g0438141' => 'han', 'Haze_04288' => 'cav', 'Haze_20492' => 'cav', 'Haze_23700' => 'cav', 'Haze_26367' => 'cav', 'Hma1.2p1_0051F.1_g029480' => 'hma', 'Hma1.2p1_0643F.1_g194750' => 'hma', 'Hma1.2p1_0823F.1_g224555' => 'hma', 'Hma1.2p1_1608F.1_g293420' => 'hma', 'HPP92_006105' => 'vpl', 'HPP92_018409' => 'vpl', 'HPP92_018412' => 'vpl', 'HPP92_020826' => 'vpl', 'HPP92_025381' => 'vpl', 'Hund01520' => 'sun', 'Hund07016' => 'sun', 'Hund24831' => 'sun', 'Lalb_Chr01g0004601' => 'lal', 'Lalb_Chr02g0157181' => 'lal', 'Lalb_Chr03g0027701' => 'lal', 'Lalb_Chr04g0261001' => 'lal', 'Lalb_Chr15g0076991' => 'lal', 'Lalb_Chr18g0045281' => 'lal', 'Lj1C212T1' => 'lonja', 'Lj1g0015881' => 'lja', 'Lj1g0018234' => 'lja', 'Lj1g0026057' => 'lja', 'Lj2C1007T3' => 'lonja', 'Lj2g0015148' => 'lja', 'Lj3C811T8' => 'lonja', 'Lj3g0015755' => 'lja', 'Lj6A668G46' => 'lonja', 'Lj9A676T55' => 'lonja', 'Lsat_1_v5_gn_2_58341' => 'lsa', 'Lsat_1_v5_gn_6_16060' => 'lsa', 'Lsat_1_v5_gn_6_43340' => 'lsa', 'Manes.04G012850' => 'mes', 'Manes.08G125400' => 'mes', 'Manes.08G145300' => 'mes', 'Manes.09G160400' => 'mes', 'Mapoly0007s0275' => 'mpo', 'MBI02_g40081_MAGBIO' => 'mbi', 'MBI04_g09710_MAGBIO' => 'mbi', 'MBI10_g18062_MAGBIO' => 'mbi', 'MBI18_g08827_MAGBIO' => 'mbi', 'MBI19_g04674_MAGBIO' => 'mbi', 'MBI19_g46718_MAGBIO' => 'mbi', 'MCO02G254' => 'mco', 'MCO04G171' => 'mco', 'MD00G1051500' => 'mdo', 'MD03G1128900' => 'mdo', 'MD11G1148200' => 'mdo', 'MD11G1148300' => 'mdo', 'MD12G1004800' => 'mdo', 'MD12G1231600' => 'mdo', 'MD12G1231900' => 'mdo', 'MD14G1003300' => 'mdo', 'Medtr4g057240' => 'mtr', 'Medtr6g029200' => 'mtr', 'Medtr7g114240' => 'mtr', 'MELO3C004342.2' => 'cme', 'MELO3C008809.2' => 'cme', 'MELO3C015374.2' => 'cme', 'MELO3C026955.2' => 'cme', 'Migut.D02293' => 'egut', 'Migut.G00220' => 'egut', 'Migut.J01882' => 'egut', 'Migut.N00127' => 'egut', 'MSTRG.10046' => 'ama', 'MSTRG.21819' => 'ama', 'MSTRG.3959' => 'ama', 'MSTRG.6507' => 'ama', 'Nitab4.5_0000173g0130' => 'nta', 'Nitab4.5_0000394g0130' => 'nta', 'Nitab4.5_0000658g0060' => 'nta', 'Nitab4.5_0002884g0060' => 'nta', 'Nitab4.5_0003067g0030' => 'nta', 'Nitab4.5_0004871g0010' => 'nta', 'Nn2g13855' => 'nnu', 'Nn3g21278' => 'nnu', 'Nn4g26049' => 'nnu', 'Nn6g35223' => 'nnu', 'Nn7g35875' => 'nnu', 'Oeu003221.2' => 'oeu', 'Oeu020202.1' => 'oeu', 'Oeu034520.2' => 'oeu', 'Oeu044798.1' => 'oeu', 'Oeu064910.1' => 'oeu', 'Os03g0219200' => 'osa', 'Os03g0351500' => 'osa', 'Os07g0665200' => 'osa', 'Os08g0561700' => 'osa', 'Peaxi162Scf00071g00745' => 'pax', 'Peaxi162Scf00463g00133' => 'pax', 'Peaxi162Scf00983g00213' => 'pax', 'Peaxi162Scf01067g00114' => 'pax', 'PGR004G1177' => 'pgr', 'PGR042G1684' => 'pgr', 'PGR083G2434' => 'pgr', 'PGR119G1565' => 'pgr', 'PGSC0003DMG400000417' => 'stu', 'PGSC0003DMG400010660' => 'stu', 'PGSC0003DMG400023086' => 'stu', 'Phvul.004G081000' => 'pvu', 'Phvul.006G097000' => 'pvu', 'Phvul.011G086300' => 'pvu', 'Potri.004G216700' => 'ptr', 'Potri.005G044400' => 'ptr', 'Potri.009G005100' => 'ptr', 'Potri.013G031100' => 'ptr', 'Potri.013G056900' => 'ptr', 'Potri.019G035800' => 'ptr', 'Pp3c20_17920' => 'ppa', 'Pp3c24_4100' => 'ppa', 'Pp3c9_24840' => 'ppa', 'Pp3c9_25690' => 'ppa', 'PRCOL_00005586' => 'pco', 'Prupe.6G112800' => 'ppe', 'Prupe.6G335000' => 'ppe', 'Prupe.7G005300' => 'ppe', 'Psat1g095440' => 'psa', 'Psat3g008560' => 'psa', 'Psat7g191600' => 'psa', 'PSO170G5251' => 'pso', 'PSO339G0003' => 'pso', 'PSO339G2292' => 'pso', 'PSO384G4938' => 'pso', 'PSO445G0022' => 'pso', 'PSO742G0001' => 'pso', 'PSO801G0219' => 'pso', 'QL01p015008' => 'qlo', 'QL03p000928' => 'qlo', 'QL03p001250' => 'qlo', 'QL03p063603' => 'qlo', 'QL07p018530' => 'qlo', 'RcHm_v2.0_Chr1g0333961' => 'rch', 'RcHm_v2.0_Chr2g0126391' => 'rch', 'RcHm_v2.0_Chr3g0452901' => 'rch', 'RcHm_v2.0_Chr3g0485841' => 'rch', 'RcHm_v2.0_Chr3g0496871' => 'rch', 'RcHm_v2.0_Chr4g0402041' => 'rch', 'RcHm_v2.0_Chr5g0056701' => 'rch', 'Rhsim01G0210600' => 'rsi', 'Rhsim04G0091600' => 'rsi', 'Rhsim04G0215500' => 'rsi', 'Rhsim07G0176700' => 'rsi', 'Rhsim13G0100500' => 'rsi', 'Sabra04G0147400' => 'sbr', 'Sabra05G0041200' => 'sbr', 'Sabra05G0116300' => 'sbr', 'Sabra09G0002300' => 'sbr', 'Sabra13G0030300' => 'sbr', 'Sabra13G0050600' => 'sbr', 'Sabra16G0057300' => 'sbr', 'Sabra18G0024600' => 'sbr', 'SalBow2G2402' => 'sbo', 'SalBow5G0307' => 'sbo', 'SalBow5G3657' => 'sbo', 'SalBow6G1068' => 'sbo', 'SalBow6G2166' => 'sbo', 'Sc06g0003500' => 'sci', 'Sc06g0003510' => 'sci', 'Sc21g0000320' => 'sci', 'Sc25g0005010' => 'sci', 'Sed0017146' => 'sed', 'Sed0017763' => 'sed', 'Sed0019115' => 'sed', 'SEGI_07649' => 'sgi', 'SEGI_15153' => 'sgi', 'SEGI_34659' => 'sgi', 'SGA_v2.0_scaffold277G46694' => 'sas', 'SGA_v2.0_scaffold57G20263' => 'sas', 'SGA_v2.0_scaffold69G23027' => 'sas', 'SGA_v2.0_scaffold89G27560' => 'sas', 'SMO143G0302' => 'smo', 'SMO169G0192' => 'smo', 'SMO197G0062' => 'smo', 'SMO340G0225' => 'smo', 'Solyc01g067740.3' => 'sly', 'Solyc03g062890.3' => 'sly', 'Solyc11g066390.2' => 'sly', 'Sopen01g029690' => 'spe', 'Sopen03g015170' => 'spe', 'Sopen11g026140' => 'spe', 'Sp1g07470' => 'spa', 'Sp4g11000' => 'spa', 'Sp6g26210' => 'spa', 'TAR369G0490' => 'tar', 'TAR369G0901' => 'tar', 'TAR623G1214' => 'tar', 'THA.LOC104802873' => 'tha', 'THA.LOC104805838' => 'tha', 'THA.LOC104815734' => 'tha', 'THA.LOC104823740' => 'tha', 'THA.LOC104826391' => 'tha', 'Thecc.05G248700' => 'tca', 'Thecc.05G252300' => 'tca', 'Thecc.09G232400' => 'tca', 'Thecc.09G298500' => 'tca', 'Thhalv10008927m.g' => 'esa', 'Thhalv10014873m.g' => 'esa', 'Thhalv10017094m.g' => 'esa', 'TPR.G33102' => 'tpr', 'TPR.G36757' => 'tpr', 'TPR.G40476' => 'tpr', 'TPR.G9143' => 'tpr', 'TWI34G1762' => 'twi', 'TWI56G1134' => 'twi', 'TWI79G1033' => 'twi', 'TWI79G1158' => 'twi', 'unitig_32.g10787' => 'ugi', 'unitig_748.g8366' => 'ugi', 'vmacro03253' => 'vma', 'vmacro05062' => 'vma', 'vmacro08214' => 'vma', 'vmacro09132' => 'vma', 'vmacro14390' => 'vma', 'vmacro15268' => 'vma', 'vmacro23265' => 'vma', 'VMungo0464G1525' => 'vmu', 'VMungo0540G0494' => 'vmu', 'VMungo1080G0393' => 'vmu', 'VMungo1127G0649' => 'vmu', 'Zm00001eb008850' => 'zma', 'Zm00001eb016940' => 'zma', 'Zm00001eb039000' => 'zma', 'Zm00001eb330020' => 'zma', 'Zm00001eb394700' => 'zma' ) $gf_id = 'HOM05D001405' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001405' ) $data_identifier = 'HOM05D001405' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 5, 'arhy' => (int) 17, 'ath' => (int) 3, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 5, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 1, 'ccl' => (int) 7, 'cil' => (int) 9, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 9, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mco' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 8, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'smo' => (int) 4, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 7, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb394700' $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